Contacts of the helix formed by residues 153 - 172 (chain A) in PDB entry 3ELY
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 153 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A SER* 2.9 16.8 + - - +
152A SER* 1.3 80.0 + - - +
154A PRO* 1.4 68.6 - - - +
155A LEU* 3.0 36.6 + - - +
156A VAL* 3.3 20.3 + - + +
157A GLU* 3.2 19.4 + - - +
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Residues in contact with PRO 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLU* 5.9 1.6 - - + +
13A LYS* 4.4 16.4 - - + -
17A ASN* 5.2 1.3 - - - +
152A SER 3.4 10.5 - - - +
153A ASN* 1.4 86.1 - - - +
155A LEU* 1.3 64.1 + - + +
157A GLU* 3.1 3.0 + - + +
158A ARG 2.9 25.1 + - - -
187A TYR* 4.0 18.6 - - + +
188A HIS* 3.1 28.4 + - + -
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Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ASN* 3.0 13.4 + - - +
154A PRO* 1.3 83.5 - - + +
156A VAL* 1.3 63.8 + - - +
158A ARG* 3.5 39.2 - - + +
159A ASP* 3.1 36.4 + - - +
188A HIS* 4.8 6.3 - - + -
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Residues in contact with VAL 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A SER* 3.6 15.0 - - - +
153A ASN* 3.3 31.5 + - + +
154A PRO 3.3 0.4 - - - -
155A LEU* 1.3 78.0 - - + +
157A GLU* 1.3 62.1 + - - +
159A ASP* 3.5 5.8 + - - +
160A ARG* 3.1 60.0 + - + +
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Residues in contact with GLU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TRP* 5.4 1.9 - - - -
13A LYS* 3.4 12.9 + - - +
149A GLU 4.8 0.2 - - - +
150A SER* 3.3 13.3 + - - -
151A SER* 2.9 48.0 + - - +
153A ASN 3.2 6.3 + - - +
154A PRO 3.1 8.3 + - - +
156A VAL* 1.3 78.8 - - - +
158A ARG* 1.3 56.8 + - - +
160A ARG* 3.4 2.9 + - - +
161A THR* 2.8 34.1 + - - -
184A LEU* 3.8 27.9 - - + +
185A ALA* 3.8 13.9 - - + +
187A TYR* 3.0 23.1 + - - +
216A THR* 5.5 0.7 + - - -
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Residues in contact with ARG 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A PRO 2.9 10.0 + - - +
155A LEU* 3.5 43.1 - - - +
157A GLU* 1.3 76.8 - - - +
159A ASP* 1.3 73.7 + - - +
161A THR* 3.7 5.3 - - - -
162A MET* 3.0 39.5 + - - +
188A HIS* 3.3 42.4 + - + +
190A ASP* 3.9 33.0 + - - -
191A VAL* 4.3 2.8 - - + +
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Residues in contact with ASP 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A LEU* 3.1 24.1 + - - +
156A VAL* 3.8 6.9 - - - +
157A GLU 3.3 0.2 - - - -
158A ARG* 1.3 97.1 + - - +
160A ARG* 1.3 63.6 + - + +
162A MET* 4.0 5.6 - - - +
163A LYS* 3.2 24.3 + - - +
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Residues in contact with ARG 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A GLY* 5.8 0.4 - - - -
149A GLU* 2.7 62.4 + - - +
150A SER 3.0 18.2 + - - -
151A SER* 3.9 6.3 - - - -
156A VAL* 3.1 37.2 + - + +
157A GLU 3.4 4.0 + - - +
159A ASP* 1.3 72.8 - - + +
161A THR* 1.3 65.0 + - - +
163A LYS* 3.5 3.6 + - - +
164A VAL* 3.1 28.0 + - - +
184A LEU* 4.4 6.7 - - + -
5465A PEG 3.3 39.5 + - - +
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Residues in contact with THR 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A GLU 2.8 21.1 + - - -
158A ARG* 3.7 4.9 - - - -
160A ARG* 1.3 73.6 - - - +
162A MET* 1.3 64.3 + - - +
164A VAL* 3.1 8.5 + - - +
165A LEU* 3.1 25.7 + - + +
182A LYS 5.4 0.9 - - - +
183A VAL* 3.5 34.3 - - + -
184A LEU* 3.5 14.8 - - - +
185A ALA* 3.1 21.0 + - - +
191A VAL* 3.6 23.1 - - + -
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Residues in contact with MET 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ARG* 3.0 27.1 + - - +
159A ASP* 4.0 6.1 - - - +
161A THR* 1.3 75.3 - - - +
163A LYS* 1.3 57.5 + - - +
165A LEU* 3.2 7.1 + - - +
166A GLU* 2.9 55.7 + - - +
190A ASP* 3.8 39.3 - - + +
191A VAL* 4.0 11.4 - - + -
194A LYS* 3.9 28.7 - - + -
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Residues in contact with LYS 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A PHE* 4.0 49.6 + - + +
134A THR* 6.3 0.8 - - - +
159A ASP 3.2 16.3 + - - +
160A ARG* 3.7 6.1 - - - +
161A THR 3.2 0.2 - - - -
162A MET* 1.3 80.4 - - - +
164A VAL* 1.3 61.3 + - - +
166A GLU* 3.5 18.2 + - + +
167A ASN* 3.1 26.2 + - - +
5465A PEG 4.8 0.9 - - - +
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Residues in contact with VAL 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A PHE* 4.2 10.5 - - + -
145A CYS* 4.1 14.1 - - - -
147A ILE* 3.5 42.0 - - + +
148A GLY* 4.9 0.7 - - - -
160A ARG 3.1 14.8 + - - +
161A THR* 3.1 11.7 + - - +
163A LYS* 1.3 76.6 - - - +
165A LEU* 1.3 57.6 + - + +
167A ASN* 3.4 4.2 + - - +
168A PHE* 3.0 26.7 + - - +
181A VAL* 3.7 15.9 - - + -
182A LYS 3.7 23.1 - - - +
5465A PEG 3.7 7.6 - - - +
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Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A THR* 3.1 22.1 + - + +
162A MET* 3.7 7.6 - - - +
164A VAL* 1.3 72.6 - - - +
166A GLU* 1.3 63.9 + - - +
168A PHE* 3.5 5.8 + - + +
169A GLU* 3.3 22.3 + - - +
181A VAL* 4.5 16.4 - - + -
182A LYS 4.8 2.9 - - - +
183A VAL* 4.2 14.6 - - + -
191A VAL* 4.1 26.0 - - + -
194A LYS* 3.8 33.5 - - + -
195A LEU* 4.1 26.7 - - + +
198A LEU* 4.2 18.1 - - + +
221A TYR* 5.2 2.9 - - + -
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Residues in contact with GLU 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A MET* 2.9 46.6 + - - +
163A LYS* 3.8 23.9 + - + +
165A LEU* 1.3 76.2 - - - +
167A ASN* 1.3 61.4 + - - +
169A GLU* 3.7 6.3 + - - +
170A ARG* 3.4 18.9 + - - +
194A LYS* 3.8 25.2 + - - +
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Residues in contact with ASN 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 4.3 6.3 - - - +
132A VAL* 3.0 33.7 + - - +
133A PHE* 3.6 20.0 - - + +
145A CYS* 5.6 3.4 - - - -
163A LYS* 3.1 18.4 + - + +
164A VAL 3.8 4.2 + - - +
165A LEU 3.3 0.2 - - - -
166A GLU* 1.3 76.3 - - - +
168A PHE* 1.3 59.7 + - - +
170A ARG* 2.9 39.9 + - - +
171A TRP* 3.0 41.8 + - - +
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Residues in contact with PHE 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LEU* 5.7 2.9 - - + -
143A LEU* 3.7 23.6 - - + -
145A CYS* 5.7 5.8 - - + -
164A VAL 3.0 16.3 + - - +
165A LEU* 3.7 9.0 - - + +
166A GLU 3.4 0.2 - - - -
167A ASN* 1.3 77.7 - - - +
169A GLU* 1.3 59.9 + - - +
171A TRP* 3.1 5.9 + - - +
172A LYS* 2.9 38.7 + - + +
179A PHE* 3.6 44.4 - + + -
181A VAL* 3.1 37.0 - - + -
198A LEU* 4.4 11.9 - - + -
202A PHE* 4.0 17.5 - + - -
221A TYR* 3.8 21.8 - + - -
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Residues in contact with GLU 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A LEU 3.3 12.2 + - - +
166A GLU* 3.8 7.6 - - - +
168A PHE* 1.3 82.8 - - - +
170A ARG* 1.3 61.9 + - - +
171A TRP 3.5 0.3 + - - -
172A LYS* 3.6 13.3 + - - +
194A LYS* 3.1 27.2 + - - -
197A ARG* 3.5 21.0 + - - +
198A LEU* 3.5 24.3 - - + +
201A ARG* 4.7 13.8 + - - +
202A PHE* 4.3 20.4 - - + -
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Residues in contact with ARG 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A VAL 2.9 28.5 + - - -
133A PHE 3.0 19.0 + - - -
134A THR* 4.4 4.3 + - - -
135A MET 3.1 26.3 + - - -
136A PRO* 4.8 1.4 - - - +
137A THR* 3.5 31.5 + - + +
166A GLU 3.4 10.8 + - - +
167A ASN* 2.9 25.0 + - - +
168A PHE 3.3 0.4 - - - -
169A GLU* 1.3 79.8 - - - +
171A TRP* 1.3 63.6 + - - +
172A LYS 4.7 1.4 - - - +
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Residues in contact with TRP 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A LEU* 3.6 30.7 - - + -
80A LEU* 3.8 30.5 - - + +
103A TYR* 4.3 16.8 - + - -
132A VAL* 3.1 20.3 + - + -
135A MET* 3.9 18.6 - - + -
136A PRO 3.7 24.0 - - - -
137A THR* 3.8 18.6 + - + +
138A GLU* 3.4 38.9 - - + +
140A SER* 5.3 2.1 + - - -
143A LEU* 3.7 20.0 - - + +
167A ASN* 3.0 44.3 + - - +
168A PHE 3.1 4.4 + - - +
170A ARG* 1.3 83.3 - - - +
172A LYS* 1.3 64.1 + - - +
173A HIS* 3.2 6.6 + - - +
176A THR* 4.7 0.5 + - - -
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Residues in contact with LYS 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A LEU* 3.8 11.2 - - + +
168A PHE* 2.9 25.4 + - + +
169A GLU 3.6 10.9 + - - +
170A ARG 3.5 2.7 - - - +
171A TRP* 1.3 75.5 - - - +
173A HIS* 1.3 72.8 + - - +
174A VAL* 4.9 4.8 + - - +
176A THR* 2.8 36.7 + - + -
179A PHE* 3.9 20.4 - - - -
202A PHE* 3.5 54.6 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il